AMBER Archive (2009)

Subject: Re: [AMBER] Specifying improper dihedrals

From: Ben Roberts (roberts_at_qtp.ufl.edu)
Date: Wed Jun 17 2009 - 14:18:41 CDT

Hi Bill,

I wasn't talking about parm.dat or frcmod files, but rather the final
prmtop. As it happened, the improper dihedrals I added I couldn't
specify there anyway; they're the ones I emailed the list about the
other day which span residue boundaries in unconventional ways.

Sorry for any confusion.

Cheers,
Ben

On 17/6/2009, at 1:56 p.m., Bill Ross wrote:

>> my solution was to reverse the atom index order in the dihedral
>
> I believe that with impropers the 3rd atom needs to be the central
> one, at least in parm.dat/frcmod files. So I would maintain this
> convention.
>
> Bill

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